Search Results (138)

Osteoclastogenesis—the activation and differentiation of osteoclasts—is one of the pivotal processes of bone remodeling and is regulated by RANKL/RANK signaling, the decoy function of osteoprotegerin (OPG), and a cascade of pro- and anti-inflammatory cytokines. The disruption of this balance leads to pathological bone loss in diseases such as osteoporosis and rheumatoid arthritis. FFAR4 (Free Fatty Acid Receptor 4), a G protein-coupled receptor for long-chain omega-3 fatty acids, has been confirmed as a key mediator of metabolic and anti-inflammatory effects. This review focuses on how FFAR4 acts as the selective receptor for the omega-3 fatty acid docosahexaenoic acid (DHA). It activates two divergent signaling pathways. The Gαq-dependent cascade facilitates intracellular calcium mobilization and ERK1/2 activation. Meanwhile, β-arrestin-2 recruitment inhibits NF-κB. These collective actions reshape the cytokine environment. In macrophages, DHA–FFAR4 signaling lowers the levels of TNF-α, interleukin-6 (IL-6), and IL-1β while increasing IL-10 secretion. Consequently, the activation of NFATc1 and NF-κB p65 is profoundly suppressed under TNF-α or RANKL stimulation. Additionally, DHA modulates the RANKL/OPG axis in osteoblastic cells by suppressing RANKL expression, thereby reducing osteoclast differentiation in an inflammatory mouse model. Full article

Introduction: Celiac disease (CD) impairs bone development in children through inflammation and nutrient malabsorption. Osteoprotegerin (OPG), a decoy receptor for RANKL, plays a role in bone remodeling and is increasingly recognized as a potential biomarker of bone metabolism and inflammation. However, its clinical significance in pediatric CD remains unclear. Aim: To evaluate the relationship between OPG levels, growth parameters, and delayed bone age in children with CD, and to assess OPG’s potential as a biomarker of bone health and disease activity. Methods: This three-year case–control study included 146 children: 25 with newly diagnosed CD (Group A), 54 with established CD on a gluten-free diet (Group B), and 67 healthy controls (Group C). Participants underwent clinical, anthropometric, and laboratory assessments at baseline and after 6 months (Groups A and B). OPG and osteocalcin were measured, and bone age was assessed radiologically. Statistical analyses included ANOVA, Spearman’s correlations, and binomial logistic regression. Results: OPG levels were highest in newly diagnosed children (Group A), showing a non-significant decrease after gluten-free diet initiation. OPG correlated negatively with age and height in CD patients and controls, and positively with hemoglobin and iron in Group B. Logistic regression revealed no significant predictive value of OPG for delayed bone age, although a trend was observed in Group B (p = 0.091). Children in long-term remission exhibited bone maturation patterns similar to healthy peers. Conclusions: OPG levels reflect disease activity and growth delay in pediatric CD but lack predictive power for delayed bone age. While OPG may serve as a secondary marker of bone turnover and inflammatory status, it is not suitable as a standalone biomarker for skeletal maturation. These findings highlight the need for integrative biomarker panels to guide bone health monitoring in children with CD. Full article

Glaesserella parasuis (G. parasuis) causes vascular inflammation in piglets, resulting in vascular damage. However, the mechanism causing vascular inflammation remains unclear. Baicalin possesses an anti-inflammatory function. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) has been implicated in immunosuppression. CD163, a scavenger receptor expressed on macrophages that acts as a decoy receptor for TWEAK, plays a crucial role in the regulation of autophagy and inflammation. This research investigated the efficacy of baicalin in reducing immunosuppression elicited by G. parasuis through the regulation of CD163/TWEAK-mediated autophagy. The data demonstrated that G. parasuis altered routine blood indicators and biochemical parameters, increased cytokine production, and induced blood vessel tissue damage. G. parasuis reduced the CD3+ T cell proportion, CD3+CD4+ T cell proportion, and CD3+CD8+ T cell proportion in piglet blood. The proteomic analysis revealed that CD163 was differentially expressed in the blood vessels of challenged piglets. Baicalin was found to regulate CD163/TWEAK axis expression, inhibit Notch/Wnt signaling pathway activation, promote autophagy, and reduce NLRP3/Caspase 1 signaling pathway activation. Baicalin also decreased cytokine production and alleviated pathological tissue damage in the blood vessels of G. parasuis-challenged piglets. Taken together, this study indicates that baicalin alleviates G. parasuis-induced immunosuppression and might promote CD163/TWEAK-mediated autophagy. This finding suggests that baicalin could serve as a potential therapeutic agent to control G. parasuis infection and related vascular inflammation. Full article

Background/Objectives: In the tumor microenvironment, hypoxia regulates genes that support tumor cell invasion and angiogenesis under the control of the hypoxia-inducible transcription factors (HIFs). Pleiotrophin (PTN) is a secreted protein that activates cell migration in endothelial and cancer cells that express α_νβ₃ integrin but has inhibitory effects in cells that do not express α_νβ₃ integrin. In both cases, the protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) seems to mediate the effects of PTN. In the present work, we studied the effect of hypoxia on PTN and PTPRZ1 expression and the functional consequences of this effect. Methods: Western blot, quantitative real-time PCR, and luciferase assays were used to study the impact of hypoxia at the protein, mRNA, and transcriptional levels, respectively. Decoy oligonucleotides (ODNs), siRNA technology, and plasmid overexpression were used to study the involvement of the transcription factors studied. Functional assays were used to study the effect of hypoxia on cell proliferation and migration. Results: Hypoxia increases PTN expression through the transcriptional activation of the corresponding gene in α_νβ₃ integrin-expressing cells. The transcription factors HIF-1α, HIF-2α, and AP-1 mediate the up-regulation of PTN by hypoxia. Functional assays in endothelial cells from PTN knockout mice or endothelial and cancer cells following the downregulation of PTN expression showed that PTN negatively affects chemical hypoxia-induced cell proliferation and migration. In cancer cells that do not express α_νβ₃ integrin, hypoxia or chemical hypoxia inhibits PTN expression in a HIF-1α-, HIF-2α-, and AP-1-independent manner. The expression of PTPRZ1 is up-regulated by chemical hypoxia, is HIF-1α- and HIF-2α-dependent, and seems to limit the activation of HIF-1α, at least in endothelial cells. Conclusions: Hypoxia or chemical hypoxia regulates PTN and PTPRZ1 expressions to restrict the stimulatory effects of hypoxia on endothelial and cancer cell migration. Full article

FGFRL1 (fibroblast growth factor receptor-like 1) is a newly identified member of the FGFR family. Its extracellular domain resembles the four conventional FGFRs, while its intracellular part lacks the tyrosine kinase domain necessary for FGF-mediated signal transduction. At first, it was only considered a “decoy receptor”. However, recent studies have demonstrated that FGFRL1 is a multifunctional molecule involved in prenatal and postnatal growth of cartilage and osteogenesis, the development of embryonic kidney and diaphragm, the modulation of cellular biological behaviors, and cell signal transduction. The functional abnormalities of FGFRL1 contribute to human diseases including congenital disease, hypertension, osteoporosis, degenerative diseases of the central nervous system, and different kinds of tumors. The present review summarizes the research progress of FGFRL1, especially its subcellular location, molecular function, and associated human disease. These data may offer valuable resources for further studying the molecular function of FGFRL1 and disclosing the mechanism of its related human diseases. Full article

The issue of antibiotic-resistant bacterial infections, coupled with the rise in viral pandemics and the slow development of new antibacterial and antiviral treatments, underscores the critical need for novel strategies to mitigate the spread of drug-resistant pathogens, enhance the efficacy of existing therapies, and accelerate the discovery and deployment of innovative antimicrobial and antiviral solutions. One promising approach to address these challenges is the dietary supplementation of non-digestible oligosaccharides (NDOs). NDOs, including human milk oligosaccharides (HMOs), play a vital role in shaping and sustaining a healthy gut microbiota. Beyond stimulating the growth and activity of beneficial gut bacteria, NDOs can also interact directly with pathogenic bacteria and viruses. Their antiviral and antibacterial properties arise from their unique interactions with pathogens and their ability to modulate the host’s immune system. NDOs can function as decoy receptors, inhibit pathogen growth, bind to bacterial toxins, stimulate the host immune response, exhibit anti-biofilm properties, and enhance barrier protection. However, a notable gap exists in the comprehensive assessment of in vivo and clinical data on this topic. This review aims to provide an in-depth overview of the in vivo evidence related to the antiviral and antibacterial effects of various NDOs and HMOs, with a focus on discussing their possible mechanisms of action. Full article

Background/Objectives: Accurately predicting protein–ligand binding affinity is essential in drug discovery for identifying effective compounds. While existing sequence-based machine learning models for binding affinity prediction have shown potential, they lack accuracy and robustness in pattern recognition, which limits their generalizability across diverse and novel binding complexes. To overcome these limitations, we developed GNNSeq, a novel hybrid machine learning model that integrates a Graph Neural Network (GNN) with Random Forest (RF) and XGBoost. Methods: GNNSeq predicts ligand binding affinity by extracting molecular characteristics and sequence patterns from protein and ligand sequences. The fully optimized GNNSeq model was trained and tested on subsets of the PDBbind dataset. The novelty of GNNSeq lies in its exclusive reliance on sequence features, a hybrid GNN framework, and an optimized kernel-based context-switching design. By relying exclusively on sequence features, GNNSeq eliminates the need for pre-docked complexes or high-quality structural data, allowing for accurate binding affinity predictions even when interaction-based or structural information is unavailable. The integration of GNN, XGBoost, and RF improves GNNSeq performance by hierarchical sequence learning, handling complex feature interactions, reducing variance, and forming a robust ensemble that improves predictions and mitigates overfitting. The GNNSeq unique kernel-based context switching scheme optimizes model efficiency and runtime, dynamically adjusts feature weighting between sequence and basic structural information, and improves predictive accuracy and model generalization. Results: In benchmarking, GNNSeq performed comparably to several existing sequence-based models and achieved a Pearson correlation coefficient (PCC) of 0.784 on the PDBbind v.2020 refined set and 0.84 on the PDBbind v.2016 core set. During external validation with the DUDE-Z v.2023.06.20 dataset, GNNSeq attained an average area under the curve (AUC) of 0.74, demonstrating its ability to distinguish active ligands from decoys across diverse ligand–receptor pairs. To further evaluate its performance, we combined GNNSeq with two additional specialized models that integrate structural and protein–ligand interaction features. When tested on a curated set of well-characterized drug–target complexes, the hybrid models achieved an average PCC of 0.89, with the top-performing model reaching a PCC of 0.97. GNNSeq was designed with a strong emphasis on computational efficiency, training on 5000+ complexes in 1 h and 32 min, with real-time affinity predictions for test complexes. Conclusions: GNNSeq provides an efficient and scalable approach for binding affinity prediction, offering improved accuracy and generalizability while enabling large-scale virtual screening and cost-effective hit identification. GNNSeq is publicly available in a server-based graphical user interface (GUI) format. Full article

Throughout the last 5 years, extensive research has been carried out towards the development of effective treatments for coronavirus disease 2019 (COVID-19). Regardless of the worldwide efforts, only a few drugs have passed clinical trials, and there is still a need to develop therapies, especially for those who are particularly vulnerable to a severe disease course. Maleimide-functionalized liposomes are proposed to serve as a platform for the immobilization, stabilization, and delivery of a short peptide sequence with high affinity towards severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, extensive optimizations should be performed in order to achieve features required for a reliable drug candidate, such as homogeneity of physical parameters and their long-term stability. Here, we present a step-by-step development process for maleimide-functionalized liposomes, which—once decorated with the SARS-CoV-2-binding peptide—could inhibit the infection progress of COVID-19. The main emphasis is placed on defining optimal lipid composition and formation conditions of PEGylated liposomes. We propose that the developed nanocarrier technology can be used as a universal platform for the construction of multiple antiviral agents. Full article

Introduction: Osteoprotegerin (OPG), encoded by the TNFRSF11B gene, is linked to the development of breast cancer via several pathways, including interactions with the receptor activator of nuclear factor-κB (RANK) ligands, apoptosis-inducing proteins like TRAIL, and genetic variations such as single nucleotide polymorphisms (SNPs), directly altering gene expression. This review aims to investigate the role of OPG expression in breast cancer. Methods: A comprehensive literature search was conducted using PubMed Medline, Google Scholar, and ScienceDirect. Only full-text English publications from inception to September 2024 were included. Results: Studies have demonstrated that certain SNPs in the OPG gene, specifically rs3102735 and rs2073618, are linked to a higher risk of breast cancer development. Additionally, OPG’s function as a TRAIL decoy receptor may inhibit the death of cancer cells. Furthermore, OPG in the serum and its interactions with BRCA mutations are being investigated for their potential influence on breast cancer progression. Studies have found that OPG promotes tumorigenesis by enhancing cell proliferation, angiogenesis, and aneuploidy in normal mammary epithelial cells. Moreover, OPG mediates the tumor-promoting effects of interleukin-1 beta and may serve as a biomarker for breast cancer risk, particularly in BRCA1 mutation carriers, through its role in dysregulated RANK signaling. Lastly, the use of recombinant OPG in mouse models has been found to exert anti-tumor effects. Conclusions: In this review, the role of OPG in breast cancer is examined. OPG has a multifaceted role in breast cancer tumorigenesis and exerts its effects through genetic variations (SNPs), interactions with TNF-related apoptosis-inducing ligand (TRAIL), and the modulation of the pro-tumorigenic microenvironment effects of angiogenesis, cell survival, and metastasis. Additionally, OPG’s dual role as a tumor suppressor and promoter serves as a possible therapeutic target to enhance apoptosis, limit bone metastasis, and modulate the tumor microenvironment. Whilst much is now known, further studies are necessary to fully delineate the role of OPG. Full article

The mutational drift of SARS-CoV-2 and the appearance of multiple variants, including the latest Omicron variant and its sub-lineages, has significantly reduced (and in some cases abolished) the protective efficacy of Wuhan spike-antigen-based vaccines and therapeutic antibodies. One of the most functionally constrained and thus largely invariable regions of the spike protein is the one involved in the interaction with the ACE2 receptor mediating the cellular entry of SARS-CoV-2. Engineered ACE2, both as a full-length protein or as an engineered polypeptide fragment, has been shown to be capable of preventing the host-cell binding of all viral variants and to be endowed with potent SARS-CoV-2 neutralization activity both in vitro and in vivo. Here, we report on the biochemical and antiviral properties of rationally designed ACE2 N-terminal, three-helix fragments that retain a native-like conformation. One of these fragments, designated as PRP8_3H and produced in recombinant form, bears structure-stabilizing and binding-affinity enhancing mutations in α-helix-I and in both α-helix I and II, respectively. While the native-like, unmodified three α-helices ACE2 fragment proved to be thermally unstable and without any detectable pseudovirion neutralization capacity, PRP8_3H was found to be highly thermostable and capable of binding to the SARS-CoV-2 spike receptor-binding domain with nanomolar affinity and to neutralize both Wuhan and Omicron spike-expressing pseudovirions at (sub)micromolar concentrations. PRP8_3H thus lends itself as a highly promising ACE2 decoy prototype suitable for a variety of formulations and prophylactic applications. Full article

Primary osteoporosis is closely linked to hormone deficiency, which disrupts the balance of bone remodeling. It affects postmenopausal women but also significantly impacts older men. Estrogen can promote the production of osteoprotegerin, a decoy receptor for RANKL, thereby preventing RANKL from activating osteoclasts. Furthermore, estrogen promotes osteoblast survival and function via activation of the Wnt signaling pathway. Likewise, androgens play a critical role in bone metabolism, primarily through their conversion to estrogen in men. Estrogen deficiency accelerates bone resorption through a rise in pro-inflammatory cytokines (IL-1, IL-6, TNF-α) and RANKL, which promote osteoclastogenesis. In the classic genomic pathway, estrogen binds to estrogen receptors in the cytoplasm, forming a complex that migrates to the nucleus and binds to estrogen response elements on DNA, regulating gene transcription. Androgens can be defined as high-affinity ligands for the androgen receptor; their combination can serve as a ligand-inducible transcription factor. Hormone replacement therapy has shown promise but comes with associated risks and side effects. In contrast, the non-genomic pathway involves rapid signaling cascades initiated at the cell membrane, influencing cellular functions without directly altering gene expression. Therefore, the ligand-independent actions and rapid signaling pathways of estrogen and androgen receptors can be harnessed to develop new drugs that provide bone protection without the side effects of traditional hormone therapies. To manage primary osteoporosis, other pharmacological treatments (bisphosphonates, teriparatide, RANKL inhibitors, sclerostin inhibitors, SERMs, and calcitonin salmon) can ameliorate osteoporosis and improve BMD via actions on different pathways. Non-pharmacological treatments include nutritional support and exercise, as well as the dietary intake of antioxidants and natural products. The current study reviews the processes of bone remodeling, hormone actions, hormone receptor status, and therapeutic targets of primary osteoporosis. However, many detailed cellular and molecular mechanisms underlying primary osteoporosis seem complicated and unexplored and warrant further investigation. Full article

Soluble CD163 (sCD163) is a circulating inflammatory mediator, indicative of acute and chronic, systemic and non-systemic inflammatory conditions. It is the cleavage outcome, consisting of almost the entire extracellular domain, of the CD163, a receptor expressed in monocytic lineages. Its expression is proportional to the abundance of CD163⁺ macrophages. Various mechanisms trigger the shedding of the CD163 receptor or the accumulation of CD163-expressing macrophages, inducing the sCD163 concentration in the circulation and bodily fluids. The activities of sCD163 range from hemoglobin (Hb) scavenging, macrophage marker, decoy receptor for cytokines, participation in immune defense mechanisms, and paracrine effects in various tissues, including the endothelium. It is an established marker of macrophage activation and thus participates in many diseases, including chronic inflammatory conditions, such as atherosclerosis, asthma, and rheumatoid arthritis; acute inflammatory conditions, such as sepsis, hepatitis, and malaria; insulin resistance; diabetes; and tumors. The sCD163 levels have been correlated with the severity, stage of the disease, and clinical outcome for many of these conditions. This review article summarizes the expression and role of sCD163 and its precursor protein, CD163, outlines the sCD163 generation mechanisms, the biological activities, and the known underlying molecular mechanisms, with an emphasis on its impact on the endothelium and its contribution in the pathophysiology of human diseases. Full article

The COVID-19 pandemic has overwhelmed healthcare systems and triggered global economic downturns. While vaccines have reduced the lethality rate of SARS-CoV-2 to 0.9% as of October 2024, the continuous evolution of variants remains a significant public health challenge. Next-generation medical therapies offer hope in addressing this threat, especially for immunocompromised individuals who experience prolonged infections and severe illnesses, contributing to viral evolution. These cases increase the risk of new variants emerging. This study explores miniACE2 decoys as a novel strategy to counteract SARS-CoV-2 variants. Using in silico design and molecular dynamics, blocking proteins (BPs) were developed with stronger binding affinity for the receptor-binding domain of multiple variants than naturally soluble human ACE2. The BPs were expressed in E. coli and tested in vitro, showing promising neutralizing effects. Notably, miniACE2 BP9 exhibited an average IC₅₀ of 4.9 µg/mL across several variants, including the Wuhan strain, Mu, Omicron BA.1, and BA.2 This low IC50 demonstrates the potent neutralizing ability of BP9, indicating its efficacy at low concentrations.Based on these findings, BP9 has emerged as a promising therapeutic candidate for combating SARS-CoV-2 and its evolving variants, thereby positioning it as a potential emergency biopharmaceutical. Full article

Repurposing utilizes existing drugs with known safety profiles and discovers new uses by combining experimental and computational approaches. The integration of computational methods has greatly advanced drug repurposing, offering a rational approach and reducing the risk of failure in these efforts. Recognizing the potential for drug repurposing, we employed our Iterative Stochastic Elimination (ISE) algorithm to screen known drugs from the DrugBank database. Repurposing in our hands is based on computer models of the actions of ligands: the ISE algorithm is a machine learning tool that creates ligand-based models by distinguishing between the physicochemical properties of known drugs and those of decoys. The models are large sets of “filters” made out, each, of molecular properties. We screen and score external sets of molecules (in our case- the DrugBank molecules) by our agonism and antagonism models based on published data (i.e., IC₅₀, K_i, or EC₅₀) and pick the top-scoring molecules as candidates for experiments. Such agonist and antagonist models for six G-protein coupled receptors (GPCRs) families facilitated the identification of repurposing opportunities. Our screening revealed 5982 new potential molecular actions (agonists, antagonists), which suggest repurposing candidates for the cannabinoid 2 (CB2), histamine (H1, H3, and H4), and dopamine 3 (D3) receptors, which may be useful to treat conditions such as neuroinflammation, obesity, allergic dermatitis, and drug abuse. These sets of best candidates should now be examined by experimentalists: based on previous such experiments, there is a very high chance of discovering novel highly bioactive molecules. Full article

Targeting epidermal growth factor receptor (EGFR) mutants is a promising strategy for treating non-small cell lung cancer (NSCLC). This study focused on the computational identification and characterization of potential EGFR mutant-selective inhibitors using pharmacophore design and validation by deep learning, virtual screening, ADMET (Absorption, distribution, metabolism, excretion and toxicity), and molecular docking-dynamics simulations. A pharmacophore model was generated using Pharmit based on the potent inhibitor JBJ-125, which targets the mutant EGFR (PDB 5D41) and is used for the virtual screening of the Zinc database. In total, 16 hits were retrieved from 13,127,550 molecules and 122,276,899 conformers. The pharmacophore model was validated via DeepCoy, generating 100 inactive decoy structures for each active molecule and ADMET tests were conducted using SWISS ADME and PROTOX 3.0. Filtered compounds underwent molecular docking studies using Glide, revealing promising interactions with the EGFR allosteric site along with better docking scores. Molecular dynamics (MD) simulations confirmed the stability of the docked conformations. These results bring out five novel compounds that can be evaluated as single agents or in combination with existing therapies, holding promise for treating the EGFR-mutant NSCLC. Full article